I downloaded a bam file and when running Picard ValidateSamFile option I got the following error:
ERROR ... ValidateSamFile Value for tag MC is not a String: class java.lang.Integer
When looking through the sam file I realized that the MC was as follows:
When looking the Sam specifications for MC tag it stands the following:
| Tag | Type | Description |
| MC | Z | CIGAR string for mate/next segment |
where Type Z means to be a string.
So in my bam file, the problem is that there is an integer for the MC value instead of a string.
My question is, as I just have the bam file, is there a way to fix this "bad" value for MC tag?
Just it in case it helps you, the software used for generating the bam file was the following (extracted from the header)
ID:1#72 ID:SCS ID:basecalling ID:Illumina2bam ID:bamadapterfind ID:BamIndexDecoder ID:spf ID:bwa ID:BamMerger ID:SplitBamByReadGroup ID:bamcollate2 ID:bamreset ID:bamadapterclip ID:bwa ID:scramble ID:bam12split ID:bamsort ID:AlignmentFilter ID:bamsort ID:bamstreamingmarkduplicates ID:scramble.1
I wonder whether one of the softwares used for the analyis originated the "bad" value for the MC tag........
Thanks in advance for your advice.